Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen

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Sammanfattning

We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

Originalspråkengelska
Artikelnummer218
TidskriftFrontiers in plant science
Volym10
Antal sidor18
ISSN1664-462X
DOI
StatusPublicerad - 28 feb 2019
MoE-publikationstypA1 Tidskriftsartikel-refererad

Vetenskapsgrenar

  • 1181 Ekologi, evolutionsbiologi
  • 1184 Genetik, utvecklingsbiologi, fysiologi
  • 1183 Växtbiologi, mikrobiologi, virologi

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@article{160c807901ba4dc196be19ed3beebd9b,
title = "Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen",
abstract = "We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.",
keywords = "ARTEMISIIFOLIA L., Ambrosia trifida, COMMON RAGWEED, COMPLETE CHLOROPLAST GENOME, EARLY EVOLUTION, GENETIC DIVERSITY, GLYPHOSATE RESISTANCE, HERBICIDE RESISTANCE, INVERSION VARIATION, NATIVE RANGE, RECURRENT SELECTION, chloroplast genome, genome skimming, glyphosate, herbicide resistance, invasive plants, noxious weeds, ragweed, 1181 Ecology, evolutionary biology, 1184 Genetics, developmental biology, physiology, 1183 Plant biology, microbiology, virology",
author = "Gaurav Sablok and Ali Amiryousefi and Xiaolan He and Hyv{\"o}nen, {Jaakko Tapani} and P{\'e}ter Poczai",
year = "2019",
month = "2",
day = "28",
doi = "10.3389/fpls.2019.00218",
language = "English",
volume = "10",
journal = "Frontiers in plant science",
issn = "1664-462X",
publisher = "Frontiers Media",

}

TY - JOUR

T1 - Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen

AU - Sablok, Gaurav

AU - Amiryousefi, Ali

AU - He, Xiaolan

AU - Hyvönen, Jaakko Tapani

AU - Poczai, Péter

PY - 2019/2/28

Y1 - 2019/2/28

N2 - We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

AB - We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

KW - ARTEMISIIFOLIA L.

KW - Ambrosia trifida

KW - COMMON RAGWEED

KW - COMPLETE CHLOROPLAST GENOME

KW - EARLY EVOLUTION

KW - GENETIC DIVERSITY

KW - GLYPHOSATE RESISTANCE

KW - HERBICIDE RESISTANCE

KW - INVERSION VARIATION

KW - NATIVE RANGE

KW - RECURRENT SELECTION

KW - chloroplast genome

KW - genome skimming

KW - glyphosate

KW - herbicide resistance

KW - invasive plants

KW - noxious weeds

KW - ragweed

KW - 1181 Ecology, evolutionary biology

KW - 1184 Genetics, developmental biology, physiology

KW - 1183 Plant biology, microbiology, virology

U2 - 10.3389/fpls.2019.00218

DO - 10.3389/fpls.2019.00218

M3 - Article

VL - 10

JO - Frontiers in plant science

JF - Frontiers in plant science

SN - 1664-462X

M1 - 218

ER -